On Jun 30, 2021, at 11:20 PM,
neovenatori...@gmail.com<mailto:neovenatori...@gmail.com> wrote:
This is something that seems really, really concerning because if there is a
method of using phylogenetic covariance to adjust the position of new data
points it seems like a lot of workers don’t know these methods exist, to the
point that even published papers overlook it.
I am surprised that researchers don’t know about these methods: they are
basically just like ancestral state reconstruction, but for new tips in the
tree. Everyone knows about “ancestral state reconstruction”. But if few people
recognize that the same methodology can be applied to new taxa, then it’s a
problem indeed.
Ancestral state “reconstruction” could be better called ancestral state
“estimation” or “prediction”. In a likelihood framework, we can also give
prediction intervals, for internal (ancestral) nodes in the tree as well as new
tips. Not all software handle new taxa, because it requires extending the tree,
or accepting a tree in which not all taxa have data. Taxa with missing data can
then be predicted, like any other node.
Cecile.
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